A landscape of diverse regulatory features coupled with chromatin interaction data leads to descriptive models of gene regulation. (A) As illustrated for the Cebpa locus (gene on top line), the strength of signals (proportional to the density of the gray along each track) from sequencing RNA, locations of cleavage by DNase, and chromatin immunoprecipitation of modified histones and transcription factors (named on the left and marked by distinctive icons) reveals where along the locus all these players in gene regulation are located. This panel was generated from data displayed at http://tinyurl.com/E-MTAB-3954. (B) Colocation of the transcription factors indicates the positions of at least 3 categories of protein complexes. Members of an octameric complex (a previously described heptamer2 plus TCF3) are shown as octagons of distinctive colors, members of other complexes are shown as ovals, and the RAD21 component of cohesin plus CTCF are shown as a green circle. (C) Maps of the frequency of chromatin interactions (shown as connections between purple rectangles representing HindIII fragments in the promoter Hi-C experiment in A) show that at least 3 complexes of proteins bound downstream of Cebpa interact with complexes at the promoter. Thus, one can surmise a structure with the promoter and enhancers juxtaposed in a region with transcriptional activity (indicated by the yellow-orange oval), anchored on cohesin complexes, and with intervening DNA in 3 loops of widely differing sizes.
